The 35-year-old spent almost two months in Tokyo's Tsukuba Memorial Hospital, where he was admitted on December 19th after inexplicably finding it difficult to walk.
The mystery illness was later diagnosed as lumbar discitis.
Thomson, who played 29 Tests for the All Blacks, expressed relief at his release in a social media post.
"57 days in hospital. 1 week of parole. Doctor just clears you to fly home.. Feels good man!," he said on Instagram.
"Thank you to everyone that supported me on this road to recovery."
